Introduction

Task: Seal Skull Measurements

Curator: Dr Richard Sabin, Collections Manager-Vertebrates, LS Division

This repository contains data and scripts for the analysis of skull measurements from a collection of seal skulls in the Natural History Museum, London. The raw data contain measurements of condylobasal length, zygomatic width and palatal length for 23 individuals of the species Halichoerus grypus (grey seal) collected in the British Isles. Twenty-three of the specimens were presented to the museum by Dr. H. R. Hewer (General Letter 1961/28) and two were presented by Dr. R. M. Laws. The seal skulls which were from various places in Scotland. Some of the seals had been culled.

##  [1] "2017-05-15_Photos_H.grypus"                    
##  [2] "2017-05-15_Seal_Skull_Measurements-written.JPG"
##  [3] "2017-05-15_Seal_Skull_raw.csv"                 
##  [4] "2017-05-15_Seal_Skull_raw.xlsx"                
##  [5] "2017-05-18_rmarkdowndraft_matt.Rmd"            
##  [6] "2017-05-18_Seal_Skulls.Rproj"                  
##  [7] "2017-05-18_Summary_Text.docx"                  
##  [8] "2017-05-18_Summary_Text.html"                  
##  [9] "2017-05-18_Summary_Text.Rmd"                   
## [10] "Archive"                                       
## [11] "CBL VS ZW.png"                                 
## [12] "clean_seal_skulls.R"                           
## [13] "H.grypus Poland.jpg"                           
## [14] "IMG_3698.JPG"                                  
## [15] "map_draft.rmd"                                 
## [16] "ReadMe_SealSkulls"                             
## [17] "ReadMe_SealSkulls_project.Rmd"                 
## [18] "seal_clean.csv"                                
## [19] "seal_skulls_clean.csv"                         
## [20] "seal_skulls_draft_plots.rmd"                   
## [21] "seal_skulls_metadata_shell.csv"                
## [22] "seal_skulls_metadata.csv"                      
## [23] "seal_skulls.Rmd"                               
## [24] "test_KM.Rmd"

From looking at the tags attached to each specimen, we agreed to collect the following raw data and took it in turns to measure the skulls as selected by Richard:

## # A tibble: 23 × 9
##       X1 Registration_Number   Age    Sex                       Locality
##    <int>               <chr> <int>  <chr>                          <chr>
## 1      1        1961.5.18.16   156   Male       Little Greenholm, Orkney
## 2      2        1961.5.18.12   122   Male      Muckle, Greenholm, Orkney
## 3      3        1961.5.18.01     1   Male        Downies, Kincardinshire
## 4      4        1961.5.18.17   204   Male                     North Rona
## 5      5        1961.5.18.19    10 Female                  Abertay Sands
## 6      6         1961.1.23.2    NA Female    Fianuis central, North Roma
## 7      7        1961.5.18.11   101   Male       Barrel of Butter, Orkney
## 8      8         1961.1.23.4    NA Female    Fianuis central, North Roma
## 9      9        1961.5.18.22    55 Female                  Abertay Sands
## 10    10        1961.5.18.23    72 Female London Zoo (ex. Farne Islands)
## # ... with 13 more rows, and 4 more variables: CBL <int>, ZW <dbl>,
## #   PL <dbl>, Comments <chr>

As a back up, we wrote down each measurement:

Data Processing: Clean Data

The file clean_seal_skulls.R in the git repository takes the raw data and outputs a clean version (the file seal_skulls_clean.csv), which is used in all analyses.

## # A tibble: 6 × 9
##      X1 Registration_Number   Age    Sex                    Locality   CBL
##   <int>               <chr> <int>  <chr>                       <chr> <int>
## 1     1        1961.5.18.16   156   Male    Little Greenholm, Orkney   277
## 2     2        1961.5.18.12   122   Male   Muckle, Greenholm, Orkney   311
## 3     3        1961.5.18.01     1   Male     Downies, Kincardinshire   169
## 4     4        1961.5.18.17   204   Male                  North Rona   298
## 5     5        1961.5.18.19    10 Female               Abertay Sands   195
## 6     6         1961.1.23.2    NA Female Fianuis central, North Roma   246
## # ... with 3 more variables: ZW <dbl>, PL <dbl>, Comments <chr>

Data Processing: Metadata

## # A tibble: 6 × 12
##         attributeName                                 attributeDefinition
##                 <chr>                                               <chr>
## 1 Registration_Number Unique identifier within the seal skulls collection
## 2                 Age                      Age of seal known from tagging
## 3                 Sex                                         Sex of seal
## 4            Locality                              Location of collection
## 5                 CBL                                 Condylobasal length
## 6                  ZW                                     Zygomatic width
## # ... with 10 more variables: columnClasses <chr>, numberType <chr>,
## #   unit <chr>, instrument <chr>, minimum <dbl>, maximum <dbl>,
## #   formatString <chr>, definition <chr>, code <chr>, levels <chr>

Data Analysis

##   Registration_Number age_months    Sex CBL     ZW     PL
## 1        1961.5.18.16        156   Male 277 169.91 117.52
## 2        1961.5.18.12        122   Male 311 179.65 130.74
## 3        1961.5.18.01          1   Male 169  90.33  69.96
## 4        1961.5.18.17        204   Male 298 182.00 124.42
## 5        1961.5.18.19         10 Female 195 106.82  83.92
## 6        1961.5.18.11        101   Male 295 164.71 125.57
## [1] "Registration_Number" "age_months"          "Sex"                
## [4] "CBL"                 "ZW"                  "PL"

MEAN and RANGE - AGE - Female

## [1] 160
## [1]  10 329

MEAN and RANGE - AGE - Male

## [1] 88.41667
## [1]   1 204

## [1] 138.4175
## [1] 149.325

## [1] 233
## [1] 252.9167

## [1] 99.09625
## [1] 107.41

## Analysis of Variance Table
## 
## Response: length
##           Df Sum Sq Mean Sq F value   Pr(>F)   
## ln_age     1  28942   28942  7.2662 0.009179 **
## Residuals 58 231015    3983                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Call:
## lm(formula = length ~ ln_age, data = test1)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -84.56 -50.93 -25.41  60.95 136.25 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  102.982     24.290   4.240 8.14e-05 ***
## ln_age        14.940      5.542   2.696  0.00918 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 63.11 on 58 degrees of freedom
## Multiple R-squared:  0.1113, Adjusted R-squared:  0.09601 
## F-statistic: 7.266 on 1 and 58 DF,  p-value: 0.009179
##   age_months
## 1  0.2500000
## 2  0.3080808
## 3  0.3661616
## 4  0.4242424
## 5  0.4823232
## 6  0.5404040

CBL Only

##   age_months
## 1  0.2500000
## 2  0.3080808
## 3  0.3661616
## 4  0.4242424
## 5  0.4823232
## 6  0.5404040

ZW Only

##   age_months
## 1  0.2500000
## 2  0.3080808
## 3  0.3661616
## 4  0.4242424
## 5  0.4823232
## 6  0.5404040

PL Only

##   age_months
## 1  0.2500000
## 2  0.3080808
## 3  0.3661616
## 4  0.4242424
## 5  0.4823232
## 6  0.5404040